8213 results for "canc*"

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• Non-invasive anal (pre)cancer dataset DAC

  Dac EGAC00001003635

• Synthetic longitudinal breast cancer whole-genome sequencing dataset

  Synthetic longitudinal breast cancer whole-genome sequencing dataset generated at the Barcelona Supercomputing Center (BSC). This study contains fully simulated longitudinal whole-genome sequencing data for one synthetic female breast cancer patient. It includes one matched-normal paired-end sample generated at a nominal depth of 30× and three longitudinal tumour samples generated at a nominal depth of 60×.

  Dataset EGAD50000002802

• Division of Molecular Oncology, National Cancer Center Research Institute Data Access Committee

  Dac EGAC00001001272

• RAIDs cervical cancer project

  The RAIDS project, launched by the Curie Institute in 2013, aims to molecularly characterize cervical cancer (CC) and improve patient risk stratification. As part of the Bio-RAIDS study (NCT02428842), next-generation sequencing was performed on tumor samples (whole-exome sequencing, shallow whole-genome sequencing and RNA-sequencing) identified frequent alterations, including PIK3CA (30%) and prognostic biomarkers like TERT, linked to poor progression-free survival. Over 50 clinically targetable mutations were found, offering new therapeutic opportunities. Transcriptomic analysis also linked specific genes and pathways to prognosis and tumor necrosis.

  Study EGAS50000001012

• RAIDs transcriptomic dataset

  Here, we describe molecular alterations in 270 cervical cancer patients using 270 tumor frozen samples using RNA-sequencing technology. Tumor samples were obtained from cervical tumor tissue collected at diagnosis. FASTQ files are deposited in the dataset.

  Dataset EGAD50000001479

• RAIDs Whole Exome Sequencing dataset

  Here, we describe molecular alterations in 291 cervical cancer patients using 291 paired tumor and constitutional frozen samples sequenced using Whole Exome Sequencing technology. Tumor samples were obtained from cervical tumor tissue collected at diagnosis. FASTQ files are deposited files are deposited in the dataset

  Dataset EGAD50000001480

• RAIDs shallow Whole Genome Sequencing dataset

  shallow Whole Genome sequencing of 302 patients with cervival cancer. Tissue cervical cancer at diagnosis....

  Dataset EGAD50000001481

• Colorectal Cancer, NDS Oxford

  Data Access Committee governing the terms on which access will be granted to the genotype data generated within the Colorectal Cancer studies research group at the Nuffield Department of Surgical Sciences (NDS), University of Oxford.

  Dac EGAC50000001075

• Mutational order shapes cell state and chromatin accessibility during early colorectal cancer evolution

  Using CRISPR mediated gene editing in patient-derived human colon organoids, we investigate how mutational order shapes cell state and downstream phenotype. We find that loss of FBXW7 on a wild-type background produces minimal phenotypic or transcriptomic change but induces a subtle shift towards a foetal-like, regenerative stem cell identity. Strikingly, the order of mutation acquisition produces markedly different outcomes. 'FA' organoids (i.e. FBXW7 loss preceding APC mutation) retain a near-normal morphology and transcriptional profile. In contrast, 'AF' organoids adopt a proliferative stem cell state and a more transformed phenotype, despite identical final genotype. These differences were associated with distinct chromatin accessibility landscapes, and reflect a cell state-dependent constraint on the transcriptional consequences of subsequent mutations.

  Study EGAS50000001945

• RNA-seq of Breast Cancer Cells in Bone-Mimetic Matrices

  Bulk RNA sequencing dataset of four breast cancer cell lines (MDA-MB-231, SCP2, MCF7 and BT-4747) cultured in collagen or in collagen-hydroxyapatite (bone mimetic) matrices to model microenvironment-driven gene expression changes.

  Study EGAS50000001966

• RNA sequencing of breast cancer cells in collagen and mineralized matrices

  The dataset includes 45 FASTQ files generated from RNA sequencing (RNA-seq) of breast cancer cells cultured in monolayer, 3D collagen and 3D mineralized extracellular matrices. RNA-seq libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina). Sequencing was performed on Illumina NextSeq 550 System using NextSeq 500/550 High-Output v2.5 Kit - 150 cycles (Illumina)

  Dataset EGAD50000002847

• MD Anderson Data Access Committee: Pembrolizumab in Advanced Rare Cancers

  Dac EGAC50000000860

• Immune-driven response to chemoradiotherapy in POLE-mutated rectal cancer

  This study aimed to investigate the chemoradiotherapy response and potential molecular mechanisms underlying chemoradiotherapy response in POLE exonuclease domain mutation-positive rectal cancer.

  Study JGAS000919

• Research on constructing a genome analysis database for malignant tumors

  Germline pathogenic variants (GPVs) in BRCA1/2 are established cancer predisposition factors; however, their biological and clinical significance in gastric cancer (GC) remain unclear. In particular, the directionality and evolutionary timing of locus-specific loss of heterozygosity (LOH) and their relationships with homologous recombination deficiency (HRD) have not been systematically examined in BRCA1/2-associated GC. We conducted integrative genomic analyses of four GCs from BRCA1/2 GPV carriers using tumour-normal tissue paired whole-exome sequencing and allele-specific copy number profiling. LOH directionality was inferred by integrating the variant allele fraction, tumour purity, and locus-specific copy number. The relative timing of LOH events during tumour evolution was estimated, and HRD was evaluated using genome instability scores and mutational signature analyses.

  Study JGAS000920

• Malignancy of breast cancer cells is increased in a luminal-hybrid state defined by progenitor markers CD146 and keratin 14

  We first analyzed a patient-derived xenograft (PDX)-derived breast cancer cell line by dividing cell populations based on CD146-expression by FACS and found that this marker defines a cellular state with increased expression of a selection of luminal hybrid markers, including KRT14. We then knocked out CD146 or KRT14 in another patient-derived xenograft (PDX)-derived breast cancer cell line to investigate further the role of these markers in the hybrid state. For all these populations, we studied their gene expression by bulk RNA sequencing.

  Study EGAS50000001972

• Transcriptomic characterization of breast cancer cells in a luminal-hybrid state

  Background: We have previously identified a subset of early human breast epithelial progenitors that, despite their luminal affiliation, are enriched for basal markers, including CD146 and keratin 14 (K14). This simultaneous presence of both lineages thus defines a luminal-hybrid state. As luminal progenitors are generally proposed as a cell of origin of breast carcinoma, we examined how cells within this luminal hybrid state relate to breast cancer malignancy. Findings: We first analyzed two patient-derived xenograft (PDX)-derived breast cancer cell lines by dividing cell populations based on CD146-expression by FACS and found that this marker defines a cellular state with increased expression of a selection of luminal hybrid markers, including KRT14. When subjecting the sorted cells to in vitro transwell filter analysis, CD146HI/K14HI luminal hybrid state cells were less invasive. Knocking out either CD146- or K14-expression by CRISPR/Cas9 on a CD146/K14-positive background did not affect the in vivo tumorigenic potential, nor the differentiation state. However, when subjecting the respective sorted populations to a soft agar colony formation assay or as in vivo xenografts, CD146HI/K14HI cells exhibited more growth and metastasis, suggesting that the luminal hybrid state contributes to malignant properties. Conclusions: Our findings demonstrate that multiple components of the luminal hybrid state provide distinct properties to tumor malignancy. The fact that breast cancer can reflect a significant part of the original breast gland differentiation hierarchy may add weight to the argument that the search for novel strategies for treating basal-like breast cancer should include manipulation of cellular differentiation states.

  Dataset EGAD50000002857

• NGS sequencing data of archival FFPE tumor tissue

  The aim of the study was to identify mutations in key ovarian cancer genes (BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1) in archival fresh-frozen paraffin embedded (FFPE) tumor tissue from platinum-resistant ovarian cancer patients enrolled in the phase I/II GANNET53 clinical trial. From the enrolled 133 patients, archival FFPE tissue was available and DNA was extracted thereof. The DNA samples passing quality control (n=118) were NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit (Oxford Gene Technology), which covers all exons of 7 key ovarian cancer genes for single nucleotide variants (SNV) and indels, and the Illumina MiSeq platform. For the paired-end runs, one Read 1 (R1) and one Read 2 (R2) FASTQ file were created for each sample. FASTQ files were compressed and created with the extension .fastq.gz.

  Dataset EGAD50000001371

• Tissue architecture and immune niches govern ctDNA release in colorectal cancer

  Circulating tumor DNA (ctDNA) is central to liquid biopsy-based cancer detection, yet its release into the bloodstream varies widely and remains poorly understood. To define the tissue-level determinants of ctDNA shedding in colorectal cancer (CRC), we integrated tumor-informed plasma sequencing with detailed histopathology, immunophenotyping, spatial transcriptomics, and in situ mutation detection in resectable stages (I–III). ctDNA detectability increased with tumor burden, and high ctDNA shedders exhibited a distinct architectural and microenvironmental phenotype characterized by expanded necrotic pseudolumina, frequent epithelial barrier disruption, and dense myeloid infiltration. Spatial profiling revealed stress-associated malignant programs and a myeloid-rich immune-luminal niche. In situ sequencing confirmed plasma-detected mutations within pseudoluminal debris, identifying these structures as focal reservoirs of shed DNA. These findings provide a mechanistic framework linking tissue architecture, immune remodelling, and spatially organized cell death to ctDNA release with implications for refining liquid biopsy applications.

  Study EGAS50000001941

• Type 1 interferon perturbates clonal competition by reshaping human blood development

  We studied hematopoietic stem cells, progenitors and immune cells from patients with myeloproliferative neoplasms (MPN) at baseline and following interferon-⍺ (IFN⍺) treatment, the only therapy to deplete mutated stem cells. We deployed single-cell multi-omics methods that distinguish the IFN⍺ effects on mutated stem cells from the admixed wildtype HSCs, with respect to their differentiation, transcriptomes, immunophenotypes, and chromatin accessibility.

  Study EGAS50000002009

• FGFR2b Prevalence in Biliary Tract Cancers

  Patients with intrahepatic cholangiocarcinoma (iCCA) often have limited effective treatment options after first-line therapy. Actionable driver mutations are present in only a small subset of patients with iCCA; therefore, therapeutic strategies such as antibody–drug conjugates (ADCs) that do not exclusively rely on presence of specific oncogenic mutations may be particularly attractive. However, there is a critical lack of knowledge regarding prevalent and actionable cell-surface targets in iCCA. We applied a novel isoform-resolved proteogenomic discovery framework for profiling cell surface targets and identified FGFR2b, a splicing isoform of FGFR2, as a therapeutic target in iCCA that is highly-expressed, tumor-enriched, localized to the membrane, and associated with prognosis. FGFR2b is the dominant isoform in iCCA, and it was present in all patients with FGFR2 fusions. These findings provide a strong rationale for further research and therapeutic development of FGFR2b-targeted biologics, including therapeutic antibodies and ADCs, in iCCA.

  Study EGAS50000002012

• Spatial Biology of Cancer of Unknown Primary

  Dac EGAC50000000720

• IMMUcan BC1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001587

• Studying ctDNA signal in plasam whole genome sequencing from high risk Breast Cancer patients

  We apply fragmentomics and minimal residue disease tools to find out signals from ctDNA in high risk Breat Cancer patients.

  Study EGAS50000001830

• Transcriptomics for IMMU-BC1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities. It contains gene-level counts.

  Dataset EGAD50000002269

• Variant calling for IMMU-BC1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes metastatic Triple Negative Breast Cancer (mTNBC) patients, naïve of treatment in the metastatic settings, treated in 1st line with chemotherapy or chemo-immunotherapy This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.

  Dataset EGAD50000002270